Examples with OntologyTerm org.molgenis.ontology.core.model.OntologyTerm used on opensource projects

Example 21 with OntologyTerm

use of org.molgenis.ontology.core.model.OntologyTerm in project molgenis by molgenis.

the class MappingServiceController method viewAttributeMapping.

/**
 * Displays an {@link AttributeMapping}
 *
 * @param mappingProjectId ID of the {@link MappingProject}
 * @param target           name of the target entity
 * @param source           name of the source entity
 * @param targetAttribute  name of the target attribute
 */
@GetMapping("/attributeMapping")
public String viewAttributeMapping(@RequestParam() String mappingProjectId, @RequestParam() String target, @RequestParam() String source, @RequestParam() String targetAttribute, Model model) {
    MappingProject project = mappingService.getMappingProject(mappingProjectId);
    MappingTarget mappingTarget = project.getMappingTarget(target);
    EntityMapping entityMapping = mappingTarget.getMappingForSource(source);
    AttributeMapping attributeMapping = entityMapping.getAttributeMapping(targetAttribute);
    if (attributeMapping == null) {
        attributeMapping = entityMapping.addAttributeMapping(targetAttribute);
    }
    EntityType refEntityType = attributeMapping.getTargetAttribute().getRefEntity();
    if (refEntityType != null) {
        Iterable<Entity> refEntities = () -> dataService.findAll(refEntityType.getId()).iterator();
        model.addAttribute("categories", refEntities);
    }
    Multimap<Relation, OntologyTerm> tagsForAttribute = ontologyTagService.getTagsForAttribute(entityMapping.getTargetEntityType(), attributeMapping.getTargetAttribute());
    model.addAttribute("tags", tagsForAttribute.values());
    model.addAttribute("dataExplorerUri", menuReaderService.getMenu().findMenuItemPath(DataExplorerController.ID));
    model.addAttribute("mappingProject", project);
    model.addAttribute("entityMapping", entityMapping);
    model.addAttribute("sourceAttributesSize", Iterables.size(entityMapping.getSourceEntityType().getAtomicAttributes()));
    model.addAttribute("attributeMapping", attributeMapping);
    model.addAttribute("attributes", newArrayList(dataService.getEntityType(source).getAtomicAttributes()));
    model.addAttribute("hasWritePermission", hasWritePermission(project, false));
    return VIEW_ATTRIBUTE_MAPPING;
}

Example 22 with OntologyTerm

use of org.molgenis.ontology.core.model.OntologyTerm in project molgenis by molgenis.

the class AlgorithmServiceImplIT method testWhenSourceHasMultipleMatchesThenFirstMappingGetsCreated.

@Test
public void testWhenSourceHasMultipleMatchesThenFirstMappingGetsCreated() {
    EntityType targetEntityType = entityTypeFactory.create("target");
    Attribute targetAttribute = attrMetaFactory.create().setName("targetHeight");
    targetAttribute.setDescription("height");
    targetEntityType.addAttribute(targetAttribute);
    EntityType sourceEntityType = entityTypeFactory.create("source");
    Attribute sourceAttribute1 = attrMetaFactory.create().setName("sourceHeight1");
    sourceAttribute1.setDescription("height");
    Attribute sourceAttribute2 = attrMetaFactory.create().setName("sourceHeight2");
    sourceAttribute2.setDescription("height");
    sourceEntityType.addAttributes(Arrays.asList(sourceAttribute1, sourceAttribute2));
    User owner = userFactory.create();
    owner.setUsername("flup");
    owner.setPassword("geheim");
    owner.setId("12345");
    owner.setActive(true);
    owner.setEmail("flup@blah.com");
    owner.setFirstName("Flup");
    owner.setLastName("de Flap");
    MappingProject project = new MappingProject("project", owner);
    project.addTarget(targetEntityType);
    EntityMapping mapping = project.getMappingTarget("target").addSource(sourceEntityType);
    Map<Attribute, ExplainedAttribute> mappings = ImmutableMap.of(sourceAttribute1, ExplainedAttribute.create(sourceAttribute1), sourceAttribute2, ExplainedAttribute.create(sourceAttribute2));
    LinkedHashMultimap<Relation, OntologyTerm> ontologyTermTags = LinkedHashMultimap.create();
    when(semanticSearchService.decisionTreeToFindRelevantAttributes(sourceEntityType, targetAttribute, ontologyTermTags.values(), null)).thenReturn(mappings);
    when(ontologyTagService.getTagsForAttribute(targetEntityType, targetAttribute)).thenReturn(ontologyTermTags);
    algorithmService.autoGenerateAlgorithm(sourceEntityType, targetEntityType, mapping, targetAttribute);
    assertEquals(mapping.getAttributeMapping("targetHeight").getSourceAttributes().get(0), sourceAttribute1);
}

Example 23 with OntologyTerm

use of org.molgenis.ontology.core.model.OntologyTerm in project molgenis by molgenis.

the class SemanticSearchServiceHelperTest method testCreateShouldQueryRule.

@Test
public void testCreateShouldQueryRule() {
    String multiOntologyTermIri = "http://www.molgenis.org/1,http://www.molgenis.org/2";
    OntologyTerm ontologyTerm_1 = OntologyTerm.create("http://www.molgenis.org/1", "molgenis label in the gcc");
    OntologyTerm ontologyTerm_2 = OntologyTerm.create("http://www.molgenis.org/2", "molgenis label 2 in the genetics", singletonList("label 2"));
    when(ontologyService.getOntologyTerm(ontologyTerm_1.getIRI())).thenReturn(ontologyTerm_1);
    when(ontologyService.getOntologyTerm(ontologyTerm_2.getIRI())).thenReturn(ontologyTerm_2);
    QueryRule actualShouldQueryRule = semanticSearchServiceHelper.createShouldQueryRule(multiOntologyTermIri);
    String expectedShouldQueryRuleToString = "SHOULD (DIS_MAX ('label' FUZZY_MATCH 'gcc molgenis label', 'description' FUZZY_MATCH 'gcc molgenis label'), DIS_MAX ('label' FUZZY_MATCH '2 label', 'description' FUZZY_MATCH '2 label', 'label' FUZZY_MATCH '2 genetics molgenis label', 'description' FUZZY_MATCH '2 genetics molgenis label'))";
    assertEquals(actualShouldQueryRule.toString(), expectedShouldQueryRuleToString);
    assertEquals(actualShouldQueryRule.getOperator(), QueryRule.Operator.SHOULD);
}

Example 24 with OntologyTerm

use of org.molgenis.ontology.core.model.OntologyTerm in project molgenis by molgenis.

the class SemanticSearchServiceHelperTest method testCreateTargetAttributeQueryTerms.

@Test
public void testCreateTargetAttributeQueryTerms() {
    Attribute targetAttribute_1 = attrMetaFactory.create().setName("targetAttribute 1");
    targetAttribute_1.setDescription("Height");
    Attribute targetAttribute_2 = attrMetaFactory.create().setName("targetAttribute 2");
    targetAttribute_2.setLabel("Height");
    Multimap<Relation, OntologyTerm> tags = LinkedHashMultimap.create();
    OntologyTerm ontologyTerm1 = OntologyTerm.create("http://onto/standingheight", "Standing height", "Description is not used", singletonList("body_length"));
    OntologyTerm ontologyTerm2 = OntologyTerm.create("http://onto/sittingheight", "Sitting height", "Description is not used", singletonList("sitting_length"));
    OntologyTerm ontologyTerm3 = OntologyTerm.create("http://onto/height", "Height", "Description is not used", singletonList("sature"));
    tags.put(Relation.isAssociatedWith, ontologyTerm1);
    tags.put(Relation.isRealizationOf, ontologyTerm2);
    tags.put(Relation.isDefinedBy, ontologyTerm3);
    // Case 1
    QueryRule actualTargetAttributeQueryTerms_1 = semanticSearchServiceHelper.createDisMaxQueryRuleForAttribute(Sets.newLinkedHashSet(asList("targetAttribute 1", "Height")), tags.values());
    String expecteddisMaxQueryRuleToString_1 = "DIS_MAX ('label' FUZZY_MATCH '1 targetattribute', 'description' FUZZY_MATCH '1 targetattribute', 'label' FUZZY_MATCH 'height', 'description' FUZZY_MATCH 'height', 'label' FUZZY_MATCH 'length body', 'description' FUZZY_MATCH 'length body', 'label' FUZZY_MATCH 'standing height', 'description' FUZZY_MATCH 'standing height', 'label' FUZZY_MATCH 'length sitting', 'description' FUZZY_MATCH 'length sitting', 'label' FUZZY_MATCH 'sitting height', 'description' FUZZY_MATCH 'sitting height', 'label' FUZZY_MATCH 'sature', 'description' FUZZY_MATCH 'sature', 'label' FUZZY_MATCH 'height', 'description' FUZZY_MATCH 'height')";
    assertEquals(actualTargetAttributeQueryTerms_1.toString(), expecteddisMaxQueryRuleToString_1);
    // Case 2
    QueryRule expecteddisMaxQueryRuleToString_2 = semanticSearchServiceHelper.createDisMaxQueryRuleForAttribute(Sets.newHashSet("Height"), tags.values());
    String expectedTargetAttributeQueryTermsToString_2 = "DIS_MAX ('label' FUZZY_MATCH 'height', 'description' FUZZY_MATCH 'height', 'label' FUZZY_MATCH 'length body', 'description' FUZZY_MATCH 'length body', 'label' FUZZY_MATCH 'standing height', 'description' FUZZY_MATCH 'standing height', 'label' FUZZY_MATCH 'length sitting', 'description' FUZZY_MATCH 'length sitting', 'label' FUZZY_MATCH 'sitting height', 'description' FUZZY_MATCH 'sitting height', 'label' FUZZY_MATCH 'sature', 'description' FUZZY_MATCH 'sature', 'label' FUZZY_MATCH 'height', 'description' FUZZY_MATCH 'height')";
    assertEquals(expecteddisMaxQueryRuleToString_2.toString(), expectedTargetAttributeQueryTermsToString_2);
    // Case 3
    QueryRule expecteddisMaxQueryRuleToString_3 = semanticSearchServiceHelper.createDisMaxQueryRuleForAttribute(Sets.newHashSet("targetAttribute 3"), tags.values());
    String expectedTargetAttributeQueryTermsToString_3 = "DIS_MAX ('label' FUZZY_MATCH '3 targetattribute', 'description' FUZZY_MATCH '3 targetattribute', 'label' FUZZY_MATCH 'length body', 'description' FUZZY_MATCH 'length body', 'label' FUZZY_MATCH 'standing height', 'description' FUZZY_MATCH 'standing height', 'label' FUZZY_MATCH 'length sitting', 'description' FUZZY_MATCH 'length sitting', 'label' FUZZY_MATCH 'sitting height', 'description' FUZZY_MATCH 'sitting height', 'label' FUZZY_MATCH 'sature', 'description' FUZZY_MATCH 'sature', 'label' FUZZY_MATCH 'height', 'description' FUZZY_MATCH 'height')";
    assertEquals(expecteddisMaxQueryRuleToString_3.toString(), expectedTargetAttributeQueryTermsToString_3);
}

Example 25 with OntologyTerm

use of org.molgenis.ontology.core.model.OntologyTerm in project molgenis by molgenis.

the class SemanticSearchServiceHelper method createShouldQueryRule.

/**
 * Create a boolean should query for composite tags containing multiple ontology terms
 *
 * @return return a boolean should queryRule
 */
public QueryRule createShouldQueryRule(String multiOntologyTermIri) {
    QueryRule shouldQueryRule = new QueryRule(new ArrayList<>());
    shouldQueryRule.setOperator(Operator.SHOULD);
    for (String ontologyTermIri : multiOntologyTermIri.split(COMMA_CHAR)) {
        OntologyTerm ontologyTerm = ontologyService.getOntologyTerm(ontologyTermIri);
        List<String> queryTerms = parseOntologyTermQueries(ontologyTerm);
        Double termFrequency = getBestInverseDocumentFrequency(queryTerms);
        shouldQueryRule.getNestedRules().add(createBoostedDisMaxQueryRuleForTerms(queryTerms, termFrequency));
    }
    return shouldQueryRule;
}